The Open Reading Frame TTC1157 of Thermus Thermophilus HB27 Encodes the Methyltransferase Forming N²-methylguanosine at Position 6 in TRNA

Overview

Journal RNA

Specialty Molecular Biology

Date 2012 Feb 17

PMID 22337946

Citations 10

Authors

Martine Roovers

Yamina Oudjama

Marcus Fislage

Janusz M Bujnicki

Wim Versees

Louis Droogmans

Affiliations

Soon will be listed here.

Abstract

N(2)-methylguanosine (m(2)G) is found at position 6 in the acceptor stem of Thermus thermophilus tRNA(Phe). In this article, we describe the cloning, expression, and characterization of the T. thermophilus HB27 methyltransferase (MTase) encoded by the TTC1157 open reading frame that catalyzes the formation of this modified nucleoside. S-adenosyl-L-methionine is used as donor of the methyl group. The enzyme behaves as a monomer in solution. It contains an N-terminal THUMP domain predicted to bind RNA and contains a C-terminal Rossmann-fold methyltransferase (RFM) domain predicted to be responsible for catalysis. We propose to rename the TTC1157 gene trmN and the corresponding protein TrmN, according to the bacterial nomenclature of tRNA methyltransferases. Inactivation of the trmN gene in the T. thermophilus HB27 chromosome led to a total absence of m(2)G in tRNA but did not affect cell growth or the formation of other modified nucleosides in tRNA(Phe). Archaeal homologs of TrmN were identified and characterized. These proteins catalyze the same reaction as TrmN from T. thermophilus. Individual THUMP and RFM domains of PF1002 from Pyrococcus furiosus were produced. These separate domains were inactive and did not bind tRNA, reinforcing the idea that the THUMP domain acts in concert with the catalytic domain to target a particular position of the tRNA molecule.

Citing Articles

Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA.

Hori H Genes (Basel). 2023; 14(2).

PMID: 36833309 PMC: 9957541. DOI: 10.3390/genes14020382.

Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine--) Methyltransferase (Trm11-Trm112 Complex).

Nishida Y, Ohmori S, Kakizono R, Kawai K, Namba M, Okada K Int J Mol Sci. 2022; 23(7).

PMID: 35409407 PMC: 8999500. DOI: 10.3390/ijms23074046.

Structural and functional insights into Archaeoglobus fulgidus m2G10 tRNA methyltransferase Trm11 and its Trm112 activator.

Wang C, Tran N, Jactel V, Guerineau V, Graille M Nucleic Acids Res. 2020; 48(19):11068-11082.

PMID: 33035335 PMC: 7641767. DOI: 10.1093/nar/gkaa830.

Naturally occurring modified ribonucleosides.

McCown P, Ruszkowska A, Kunkler C, Breger K, Hulewicz J, Wang M Wiley Interdiscip Rev RNA. 2020; 11(5):e1595.

PMID: 32301288 PMC: 7694415. DOI: 10.1002/wrna.1595.

Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium .

Hori H Front Genet. 2019; 10:204.

PMID: 30906314 PMC: 6418473. DOI: 10.3389/fgene.2019.00204.

References

Ishida K, Kunibayashi T, Tomikawa C, Ochi A, Kanai T, Hirata A . Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus. Nucleic Acids Res. 2010; 39(6):2304-18. PMC: 3064792. DOI: 10.1093/nar/gkq1180. View

Reyes V, Abelson J . A synthetic substrate for tRNA splicing. Anal Biochem. 1987; 166(1):90-106. DOI: 10.1016/0003-2697(87)90551-3. View

Edqvist J, Blomqvist K, Straby K . Structural elements in yeast tRNAs required for homologous modification of guanosine-26 into dimethylguanosine-26 by the yeast Trm1 tRNA-modifying enzyme. Biochemistry. 1994; 33(32):9546-51. DOI: 10.1021/bi00198a021. View

Tomikawa C, Yokogawa T, Kanai T, Hori H . N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network. Nucleic Acids Res. 2009; 38(3):942-57. PMC: 2817472. DOI: 10.1093/nar/gkp1059. View

Fislage M, Roovers M, Tuszynska I, Bujnicki J, Droogmans L, Versees W . Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life. Nucleic Acids Res. 2012; 40(11):5149-61. PMC: 3367198. DOI: 10.1093/nar/gks163. View

Andersen N, Douthwaite S . YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J Mol Biol. 2006; 359(3):777-86. DOI: 10.1016/j.jmb.2006.04.007. View

Gabant G, Auxilien S, Tuszynska I, Locard M, Gajda M, Chaussinand G . THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain. Nucleic Acids Res. 2006; 34(9):2483-94. PMC: 1459410. DOI: 10.1093/nar/gkl145. View

Sunita S, Purta E, Durawa M, Tkaczuk K, Swaathi J, Bujnicki J . Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res. 2007; 35(13):4264-74. PMC: 1934991. DOI: 10.1093/nar/gkm411. View

Sprinzl M, Vassilenko K . Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 2004; 33(Database issue):D139-40. PMC: 539966. DOI: 10.1093/nar/gki012. View

10.

Sergiev P, Bogdanov A, Dontsova O . Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Nucleic Acids Res. 2007; 35(7):2295-301. PMC: 1874633. DOI: 10.1093/nar/gkm104. View

11.

Menezes S, Gaston K, Krivos K, Apolinario E, Reich N, Sowers K . Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14. Nucleic Acids Res. 2011; 39(17):7641-55. PMC: 3177210. DOI: 10.1093/nar/gkr475. View

12.

Aravind L, Koonin E . THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. Trends Biochem Sci. 2001; 26(4):215-7. DOI: 10.1016/s0968-0004(01)01826-6. View

13.

Fislage M, Roovers M, Munnich S, Droogmans L, Versees W . Crystallization and preliminary X-ray crystallographic analysis of putative tRNA-modification enzymes from Pyrococcus furiosus and Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011; 67(Pt 11):1432-5. PMC: 3212469. DOI: 10.1107/S1744309111036347. View

14.

Armengaud J, Urbonavicius J, Fernandez B, Chaussinand G, Bujnicki J, Grosjean H . N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota. J Biol Chem. 2004; 279(35):37142-52. DOI: 10.1074/jbc.M403845200. View

15.

Pallan P, Kreutz C, Bosio S, Micura R, Egli M . Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs. RNA. 2008; 14(10):2125-35. PMC: 2553729. DOI: 10.1261/rna.1078508. View

16.

Roovers M, Hethke C, Legrain C, Thomm M, Glansdorff N . Isolation of the gene encoding Pyrococcus furiosus ornithine carbamoyltransferase and study of its expression profile in vivo and in vitro. Eur J Biochem. 1997; 247(3):1038-45. DOI: 10.1111/j.1432-1033.1997.01038.x. View

17.

Hopper A, Furukawa A, Pham H, Martin N . Defects in modification of cytoplasmic and mitochondrial transfer RNAs are caused by single nuclear mutations. Cell. 1982; 28(3):543-50. DOI: 10.1016/0092-8674(82)90209-4. View

18.

Okada K, Muneyoshi Y, Endo Y, Hori H . Production of yeast (m2G10) methyltransferase (Trm11 and Trm112 complex) in a wheat germ cell-free translation system. Nucleic Acids Symp Ser (Oxf). 2009; (53):303-4. DOI: 10.1093/nass/nrp152. View

19.

Liao H, McKenzie T, Hageman R . Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. Proc Natl Acad Sci U S A. 1986; 83(3):576-80. PMC: 322906. DOI: 10.1073/pnas.83.3.576. View

20.

Liu J, Straby K . The human tRNA(m(2)(2)G(26))dimethyltransferase: functional expression and characterization of a cloned hTRM1 gene. Nucleic Acids Res. 2000; 28(18):3445-51. PMC: 110725. DOI: 10.1093/nar/28.18.3445. View